Mapping of small RNAs in the human ENCODE regions
Mapping of small RNAs in the human ENCODE regions
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DOI：
10.1016/j.ajhg.2008.02.016
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发表时间：
2008-04-01
影响因子：
9.8
通讯作者：
Antonarakis, Stylianos E.
中科院分区：
文献类型：
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作者：
Borel, Christelle;Gagnebin, Maryline;Antonarakis, Stylianos E.
阐明小RNA的转录组对于理解基因组和细胞功能至关重要。我们在此报告了人类基因组ENCODE区域中小RNA（< 50 nt）的分析结果。用正向和反向ENCODE高密度分辨率平铺阵列对来自四种不同细胞系（HepG 2、HelaS 3、GM 06990、SK-N-SH）的大小分级RNA进行作图。前1%的杂交信号被称为SmRfrags（小RNA片段）。8%的SmRfrags与GENCODE基因（CDS）重叠，因为大多数SmRfrags映射到基因间区域（34%），内含子区域（53%）和非翻译区（UTR）（5%）。此外，5 'UTR区域中9.6%和16.8%的SmR片段分别与His/Pol II/TAF 250结合位点和DNA酶I超敏位点显著重叠（与预期的5.3%和9%相比）。有趣的是，17%-24%（取决于细胞系）的SmRfrags是有义-反义链对，显示出重叠转录的证据。在HeLa和GM 06990细胞中，基因间区SmRfrags与转录片段（Txfrags）的重叠率分别为3.4%和7.2%。我们假设，一小部分已鉴定的SmRfrags对应于microRNA。我们通过北方印迹测试了一组15个与smRfrags重叠的microRNA候选物的高可能性预测，并验证了三个潜在的microRNA（类似于20 nt长度）。值得注意的是，大多数剩余的候选者显示出更大的杂交带（类似于100 nt），其可能是microRNA前体。小RNA转录组是基因组功能的重要和丰富的组成部分。
The elucidation of the largely unknown transcriptome of small RNAs is crucial for the understanding of genome and cellular function. We report here the results of the analysis of small RNAs (< 50 nt) in the ENCODE regions of the human genome. Size-fractionated RNAs from four different cell lines (HepG2, HelaS3, GM06990, SK-N-SH) were mapped with the forward and reverse ENCODE high-density resolution tiling arrays. The top 1% of hybridization signals are termed SmRfrags (Small RNA fragments). Eight percent of SmRfrags overlap the GENCODE genes (CDS), given that the majority map to intergenic regions (34%), intronic regions (53%), and untranslated regions (UTRs) (5%). In addition, 9.6% and 16.8% of SmRfrags in the 5'UTR regions overlap significantly with His/Pol II/TAF250 binding sites and DNase I Hypersensitive sites, respectively (compared to the 5.3% and 9% expected). Interestingly, 17%-24% (depending on the cell line) of SmRfrags are sense-antisense strand pairs that show evidence of overlapping transcription. Only 3.4% and 7.2% of SmRfrags in intergenic regions overlap transcribed fragments (Txfrags) in HeLa and GM06990 cell lines, respectively. We hypothesized that a fraction of the identified SmRfrags corresponded to microRNAs. We tested by Northern blot a set of 15 high-likelihood predictions of microRNA candidates that overlap with smRfrags and validated three potential microRNAs (similar to 20 nt length). Notably, most of the remaining candidates showed a larger hybridizing band (similar to 100 nt) that could be a microRNA precursor. The small RNA transcriptome is emerging as an important and abundant component of the genome function.